/**
* Run the test.
*
* @param dbre The database to use.
* @return true if the test passed.
*/
public boolean run(DatabaseRegistryEntry dbre) {
boolean result = true;
Connection con = dbre.getConnection();
// --------------------------------
// MGI - dbprimary_acc should have MGI: prefix
int rows =
DBUtils.getRowCount(
con,
"SELECT COUNT(*) FROM external_db e, xref x WHERE x.external_db_id=e.external_db_id AND e.db_name='MGI' AND x.dbprimary_acc NOT LIKE 'MGI:%'");
if (rows > 0) {
ReportManager.problem(
this, con, rows + " MGI xrefs do not have MGI: prefixes in the dbprimary_acc column");
result = false;
} else {
ReportManager.correct(this, con, "All MGI xrefs have the correct prefix");
}
// --------------------------------
// GO - dbprimary_acc and display_label should have GO: prefix
rows =
DBUtils.getRowCount(
con,
"SELECT COUNT(*) FROM external_db e, xref x WHERE x.external_db_id=e.external_db_id AND e.db_name='GO' AND (x.dbprimary_acc NOT LIKE 'GO:%' OR x.display_label NOT LIKE 'GO:%')");
if (rows > 0) {
ReportManager.problem(
this,
con,
rows
+ " GO xrefs do not have GO: prefixes in the dbprimary_acc and/or display_label columns");
result = false;
} else {
ReportManager.correct(this, con, "All GO xrefs have the correct prefix");
}
// --------------------------------
// ZFIN - dbprimary_acc should begin with ZDB
rows =
DBUtils.getRowCount(
con,
"SELECT COUNT(*) FROM external_db e, xref x WHERE x.external_db_id=e.external_db_id AND e.db_name='ZFIN_ID' AND x.dbprimary_acc NOT LIKE 'ZDB%'");
if (rows > 0) {
ReportManager.problem(
this,
con,
rows
+ " ZFIN xrefs do not have ZDB: prefixes in the dbprimary_acc and/or display_label columns");
result = false;
} else {
ReportManager.correct(this, con, "All ZFIN xrefs have the correct prefix");
}
return result;
} // run
@Override
protected boolean runTest(DatabaseRegistryEntry dbre) {
boolean result = true;
for (Map.Entry<String, String[]> method_tags : getMandatoryTags().entrySet()) {
Vector<String> quoted_tags = new Vector<String>();
for (String t : method_tags.getValue()) {
quoted_tags.add(String.format("'%s'", t));
}
List<String> mlsss =
getTemplate(dbre)
.queryForDefaultObjectList(
String.format(
QUERY,
StringUtils.join(quoted_tags, ","),
method_tags.getKey(),
method_tags.getValue().length),
String.class);
if (mlsss.size() > 0) {
ReportManager.problem(
this,
dbre.getConnection(),
"MLSSs for "
+ method_tags.getKey()
+ " found with no statistics: "
+ StringUtils.join(mlsss, ","));
result = false;
} else {
ReportManager.correct(this, dbre.getConnection(), "PASSED ");
}
}
return result;
}
private boolean checkFeaturesAndMapWeights(Connection con) {
boolean result = true;
int rowCount = DBUtils.getRowCount(con, "SELECT COUNT(*) FROM marker_feature");
if (rowCount == 0) {
ReportManager.problem(
this, con, "No marker features in database even though markers are present");
result = false;
}
int badWeightCount =
DBUtils.getRowCount(
con,
"SELECT marker_id, COUNT(*) AS correct, map_weight FROM marker_feature GROUP BY marker_id HAVING map_weight != correct");
if (badWeightCount > 0) {
ReportManager.problem(
this,
con,
badWeightCount + " marker features have not been assigned correct map weights");
result = false;
}
if (result) {
ReportManager.correct(this, con, "Marker features appear to be ok");
}
return result;
} // checkFeaturesAndMapWeights
/**
* Run the test.
*
* @param dbre The database to use.
* @return true if the test passed.
*/
public boolean run(DatabaseRegistryEntry dbre) {
boolean result = true;
Connection con = dbre.getConnection();
int rows =
DBUtils.getRowCount(
con,
"SELECT COUNT(*) FROM external_db WHERE db_display_name IS NULL OR db_display_name LIKE ' %'");
if (rows > 0) {
ReportManager.problem(
this,
con,
rows
+ " rows in external_db have null or blank db_display_name - this will mean their label is missing on the web page");
result = false;
} else {
ReportManager.correct(this, con, "No blank db_display_name fields in external_db");
}
return result;
} // run
/** Check that all priorities are greater than a certain threshold. */
private boolean checkMarkerPriorities(Connection con) {
boolean result = true;
int count =
DBUtils.getRowCount(
con, "SELECT COUNT(*) FROM marker WHERE priority > " + MARKER_PRIORITY_THRESHOLD);
if (count == 0) {
ReportManager.problem(
this,
con,
" No marker features have priorities greater than the threshold ("
+ MARKER_PRIORITY_THRESHOLD
+ ")");
result = false;
} else {
ReportManager.correct(
this,
con,
"Some marker features have priorities greater than " + MARKER_PRIORITY_THRESHOLD);
}
return result;
}
/**
* Test various things about ditag features.
*
* @param dbre The database to use.
* @return Result.
*/
public boolean run(DatabaseRegistryEntry dbre) {
boolean result = true;
Connection con = dbre.getConnection();
int rows =
DBUtils.getRowCount(
con, "SELECT COUNT(*) FROM identity_xref WHERE cigar_line REGEXP '^[MDI]'");
if (rows > 0) {
ReportManager.problem(
this,
con,
rows + " cigar lines in identity_xref appear to be in the wrong format (number first)");
result = false;
} else {
ReportManager.correct(
this, con, "All cigar lines in identity_xref are in the correct format");
}
return result;
}
private boolean checkCodingCountAttributes(final DatabaseRegistryEntry dbre) {
boolean result = true;
Connection con = dbre.getConnection();
String code = (dbre.getType() == DatabaseType.SANGER_VEGA) ? "KnwnPCCount" : "coding_cnt";
SqlTemplate t = DBUtils.getSqlTemplate(dbre);
String sql =
"select distinct g.seq_region_id from gene g where g.biotype = ? and g.seq_region_id not in (select distinct g.seq_region_id from gene g, seq_region_attrib sa, attrib_type at where g.seq_region_id = sa.seq_region_id and sa.attrib_type_id = at.attrib_type_id and at.code in (?,?))";
List<String> toplevel =
t.queryForDefaultObjectList(sql, String.class, "protein_coding", "LRG", "non_ref");
sql =
"select distinct g.seq_region_id from gene g, seq_region_attrib sa, attrib_type at where g.seq_region_id = sa.seq_region_id and sa.attrib_type_id = at.attrib_type_id and code =? ";
List<String> known = t.queryForDefaultObjectList(sql, String.class, code);
Set<String> missing = new HashSet<String>(toplevel);
missing.removeAll(known);
if (missing.isEmpty()) {
ReportManager.correct(
this,
con,
"All seq_regions with protein_coding genes have a coding_cnt attribute associated with them");
} else {
String msg =
String.format(
"%s regions with protein_coding genes do not have the coding_cnt attribute associated",
missing.size());
ReportManager.problem(this, con, msg);
result = false;
}
return result;
}
/**
* Run the test.
*
* @param dbre The database to use.
* @return true if the test passed.
*/
public boolean run(DatabaseRegistryEntry dbre) {
boolean result = true;
Connection con = dbre.getConnection();
// list of transcript analysis logic_names which are allowed to not have supporting features
String allowed = "'" + StringUtils.join(allowedNoSupporting, "','") + "'";
String sql =
String.format(
"SELECT COUNT(*),t.analysis_id FROM transcript t LEFT JOIN transcript_supporting_feature tsf ON t.transcript_id = tsf.transcript_id JOIN analysis a ON a.analysis_id=t.analysis_id WHERE a.analysis_id=t.analysis_id and tsf.transcript_id IS NULL AND a.logic_name NOT IN (%s) group by t.analysis_id",
allowed);
int rows = DBUtils.getRowCount(con, sql);
if (rows > 0) {
ReportManager.problem(
this,
con,
rows
+ " transcripts which should have transcript_supporting_features do not have them\nUseful SQL: "
+ sql);
result = false;
} else {
ReportManager.correct(
this, con, "All transcripts that require supporting features have them");
}
return result;
} // run
/**
* Run the test.
*
* @param dbre The database to use.
* @return true if the test passed.
*/
public boolean run(DatabaseRegistryEntry dbre) {
boolean result = true;
Connection con = dbre.getConnection();
if (tableHasRows(con, "method_link_species_set")) {
/* Check if have both BLASTZ_NET and LASTZ_NET entries for the same species set */
int numOfBLASTZ_LASTZSpeciesSets =
DBUtils.getRowCount(
con,
"SELECT species_set_id, count(*) FROM method_link_species_set JOIN method_link USING (method_link_id) WHERE TYPE in ('BLASTZ_NET', 'LASTZ_NET') GROUP BY species_set_id HAVING count(*) > 1");
if (numOfBLASTZ_LASTZSpeciesSets > 0) {
ReportManager.problem(
this,
con,
"FAILED method_link_species_set table contains "
+ numOfBLASTZ_LASTZSpeciesSets
+ " entries with a BLASTZ_NET and LASTZ_NET entry for the same species_set");
ReportManager.problem(
this,
con,
"USEFUL SQL: SELECT species_set_id, count(*) FROM method_link_species_set JOIN method_link USING (method_link_id) WHERE TYPE in ('BLASTZ_NET', 'LASTZ_NET') GROUP BY species_set_id HAVING count(*) > 1");
result = false;
}
// Everything below will be ignored on the master database
if (isMasterDB(dbre.getConnection())) {
return result;
}
/* Check method_link_species_set <-> synteny_region */
/* All method_link for syntenies must have an internal ID between 101 and 199 */
result &=
checkForOrphansWithConstraint(
con,
"method_link_species_set",
"method_link_species_set_id",
"synteny_region",
"method_link_species_set_id",
"method_link_id >= 101 and method_link_id < 200");
result &=
checkForOrphans(
con,
"synteny_region",
"method_link_species_set_id",
"method_link_species_set",
"method_link_species_set_id");
} else {
ReportManager.correct(
this, con, "NO ENTRIES in method_link_species_set table, so nothing to test IGNORED");
}
return result;
}
/** Check that the schema_version in the meta table is present and matches the database name. */
private boolean checkSchemaVersionDBName(DatabaseRegistryEntry dbre) {
boolean result = true;
// get version from database name
String dbNameVersion = dbre.getSchemaVersion();
logger.finest("Schema version from database name: " + dbNameVersion);
// get version from meta table
Connection con = dbre.getConnection();
if (dbNameVersion == null) {
ReportManager.warning(this, con, "Can't deduce schema version from database name.");
return false;
}
String schemaVersion =
DBUtils.getRowColumnValue(
con, "SELECT meta_value FROM meta WHERE meta_key='schema_version'");
logger.finest("schema_version from meta table: " + schemaVersion);
if (schemaVersion == null || schemaVersion.length() == 0) {
ReportManager.problem(this, con, "No schema_version entry in meta table");
return false;
} else if (!schemaVersion.matches("[0-9]+")) {
ReportManager.problem(this, con, "Meta schema_version " + schemaVersion + " is not numeric");
return false;
} else if (!dbNameVersion.equals(schemaVersion) && !isSangerVega) { // do
// not
// report
// for
// sangervega
ReportManager.problem(
this,
con,
"Meta schema_version "
+ schemaVersion
+ " does not match version inferred from database name ("
+ dbNameVersion
+ ")");
return false;
} else {
ReportManager.correct(
this,
con,
"schema_version " + schemaVersion + " matches database name version " + dbNameVersion);
}
return result;
}
private boolean checkTableExists(Connection con) {
boolean result = true;
if (!DBUtils.checkTableExists(con, "meta")) {
result = false;
ReportManager.problem(this, con, "Meta table not present");
} else {
ReportManager.correct(this, con, "Meta table present");
}
return result;
}
private boolean tableHasRows(Connection con) {
boolean result = true;
int rows = DBUtils.countRowsInTable(con, "meta");
if (rows == 0) {
result = false;
ReportManager.problem(this, con, "meta table is empty");
} else {
ReportManager.correct(this, con, "meta table has data");
}
return result;
}
/**
* Run the test.
*
* @param dbre The database to use.
* @return true if the test passed.
*/
public boolean run(DatabaseRegistryEntry dbre) {
boolean result = true;
Connection con = dbre.getConnection();
Map tableToLetter = new HashMap();
tableToLetter.put("gene", "G");
tableToLetter.put("transcript", "T");
tableToLetter.put("translation", "P");
Iterator it = tableToLetter.keySet().iterator();
while (it.hasNext()) {
String table = (String) it.next();
String letter = (String) tableToLetter.get(table);
String regexp = "EST" + letter + "[0-9]+";
String sql =
"SELECT COUNT(*) FROM "
+ table
+ " x, analysis a WHERE a.analysis_id=x.analysis_id "
+ "AND a.logic_name LIKE '%est%' AND x.stable_id NOT REGEXP '"
+ regexp
+ "'";
if (table.equals("translation")) {
// need extra join to transcript table
sql =
"SELECT COUNT(*) FROM translation x, transcript t, analysis a WHERE a.analysis_id=t.analysis_id AND x.transcript_id=t.transcript_id AND a.logic_name LIKE '%est%' AND x.stable_id NOT REGEXP 'ESTP[0-9]+'";
}
int rows = DBUtils.getRowCount(con, sql);
if (rows > 0) {
ReportManager.problem(
this, con, rows + " " + table + " stable IDs do not contain EST" + letter);
result = false;
} else {
ReportManager.correct(this, con, "All stable IDs contain EST" + letter);
}
}
return result;
} // run
private boolean checkKeysPresent(Connection con) {
boolean result = true;
// check that certain keys exist
String[] metaKeys = {
"assembly.default",
"assembly.name",
"assembly.date",
"assembly.coverage_depth",
"species.classification",
"species.common_name",
"species.display_name",
"species.production_name",
"species.scientific_name",
"species.stable_id_prefix",
"species.taxonomy_id",
"species.url",
"repeat.analysis",
};
for (String metaKey : metaKeys) {
int rows = metaKeyCount(con, metaKey);
if (rows == 0) {
result = false;
ReportManager.problem(this, con, "No entry in meta table for " + metaKey);
}
}
// check that there are some species.alias entries
int MIN_ALIASES = 3;
int rows = metaKeyCount(con, "species.alias");
if (rows < MIN_ALIASES) {
result = false;
String msg =
String.format("Only %d species.alias entries, should be at least %d", rows, MIN_ALIASES);
ReportManager.problem(this, con, msg);
} else {
ReportManager.correct(this, con, rows + " species.alias entries present");
}
return result;
}
/**
* Check the data in the assembly_exception table. Note referential integrity checks are done in
* CoreForeignKeys.
*
* @param dbre The database to use.
* @return Result.
*/
public boolean run(DatabaseRegistryEntry dbre) {
boolean result = true;
Connection con = dbre.getConnection();
String qry =
"select count(*) from gene,transcript,translation "
+ "where gene.biotype like '%pseudogene%'"
+ " and transcript.gene_id=gene.gene_id "
+ " and translation.transcript_id=transcript.transcript_id and gene.biotype!= 'polymorphic_pseudogene' ";
if (dbre.getType()
== DatabaseType
.SANGER_VEGA) { // for sangervega ignore genes that do not have source havana or WU and
// allow
// polymorphic_pseudogene to have translations
qry += " and (gene.source='havana' or gene.source='WU')";
}
if (dbre.getType() == DatabaseType.SANGER_VEGA || dbre.getType() == DatabaseType.VEGA) {
// Vega allows translations on translated_processed_pseudogene-s
qry += " and gene.biotype != 'translated_processed_pseudogene'";
}
int rows = DBUtils.getRowCount(con, qry);
if (rows > 0) {
result = false;
ReportManager.problem(
this,
con,
"Translation table contains "
+ rows
+ " rows for pseudogene types - should contain none");
}
if (result) {
ReportManager.correct(this, con, "No pseudogenes have translations");
}
return result;
}
/**
* Run the test.
*
* @param dbre The database to use.
* @return true if the test passed.
*/
public boolean run(DatabaseRegistryEntry dbre) {
boolean result = true;
Connection con = dbre.getConnection();
try {
Statement stmt = con.createStatement();
// if this query returns anything then something is wrong
ResultSet rs =
stmt.executeQuery(
"SELECT sr.seq_region_id, sr.name FROM seq_region sr, dna d WHERE sr.seq_region_id=d.seq_region_id AND d.sequence REGEXP '[^ATGCN]'");
while (rs != null && rs.next()) {
result = false;
ReportManager.problem(
this,
con,
String.format(
"%s (seq_region_id %s) has non GTACN sequence", rs.getString(2), rs.getLong(1)));
} // while rs
stmt.close();
} catch (SQLException e) {
e.printStackTrace();
}
if (result == true) {
ReportManager.correct(this, con, "No entries in dna table have non-GTACN bases.");
}
return result;
} // run
/** Check for values containing the text ARRAY(. */
private boolean checkArrays(DatabaseRegistryEntry dbre) {
boolean result = true;
Connection con = dbre.getConnection();
try {
Statement stmt = con.createStatement();
ResultSet rs =
stmt.executeQuery(
"SELECT meta_key, meta_value FROM meta WHERE meta_value LIKE 'ARRAY(%'");
while (rs.next()) {
ReportManager.problem(
this,
con,
"Meta table entry for key "
+ rs.getString(1)
+ " has value "
+ rs.getString(2)
+ " which is probably incorrect");
result = false;
}
} catch (Exception e) {
e.printStackTrace();
}
if (result) {
ReportManager.correct(this, con, "No duplicates in the meta table");
}
return result;
}
/** Check for duplicate entries in the meta table. */
private boolean checkDuplicates(DatabaseRegistryEntry dbre) {
boolean result = true;
Connection con = dbre.getConnection();
try {
Statement stmt = con.createStatement();
ResultSet rs =
stmt.executeQuery(
"SELECT meta_key, meta_value FROM meta GROUP BY meta_key, meta_value, species_id HAVING COUNT(*)>1");
while (rs.next()) {
ReportManager.problem(
this,
con,
"Key/value pair "
+ rs.getString(1)
+ "/"
+ rs.getString(2)
+ " appears more than once in the meta table");
result = false;
}
} catch (Exception e) {
e.printStackTrace();
}
if (result) {
ReportManager.correct(this, con, "No duplicates in the meta table");
}
return result;
}
protected boolean runTestForSpecies(DatabaseRegistryEntry dbre, int speciesId) {
String productionName =
fetchSingleMetaValueFor(sqlTemplateTestDb, speciesId, "species.production_name");
String assemblyDefault =
fetchSingleMetaValueFor(sqlTemplateTestDb, speciesId, "assembly.default");
String genebuildStartDate =
fetchSingleMetaValueFor(sqlTemplateTestDb, speciesId, "genebuild.start_date");
if (!speciesConfiguredForDnaCompara(productionName)) {
getLogger()
.info(
"Skipping species "
+ productionName
+ ", because it is not linked to any method involving DNA comparisons in the compara master.");
return true;
}
getLogger().info("Testing species " + productionName);
boolean hasEntryInMasterDb =
fetchHasGenomeDbId(productionName, assemblyDefault, genebuildStartDate);
if (!hasEntryInMasterDb) {
ReportManager.correct(
this,
testDbConn,
"Species " + productionName + " has no genome_db entry in the master database.");
return true;
}
int genomeDbId = fetchGenomeDbId(productionName, assemblyDefault, genebuildStartDate);
int toplevelSeqRegionCount = fetchToplevelSeqRegionCount();
int dnaFragRowCountFor = fetchDnaFragRowCountFor(genomeDbId);
boolean sequenceCountsOk = toplevelSeqRegionCount == dnaFragRowCountFor;
if (sequenceCountsOk) {
ReportManager.correct(
this,
testDbConn,
"Sequence counts for this "
+ "species are "
+ toplevelSeqRegionCount
+ " both in "
+ "core and compara master database.");
} else {
ReportManager.problem(
this,
testDbConn,
"Sequence counts for this "
+ "species are "
+ toplevelSeqRegionCount
+ " toplevel "
+ "sequence regions in the core database and "
+ dnaFragRowCountFor
+ " dna frags in the compara "
+ "master database. The counts should be equal.\n"
+ "This can happen, if the assembly has been changed, "
+ "but the assembly.default entry in the meta table has "
+ "not been changed. In that case the dna_frag table in "
+ "the compara master database is not updated "
+ "by the populate_mdb.pl script.");
}
boolean allToplevelSeqRegionInDnaFragTable = assertToplevelSeqRegionInDnaFragTable(genomeDbId);
return sequenceCountsOk && allToplevelSeqRegionInDnaFragTable;
}
/** Check that all chromomes have > 0 markers_map_locations and marker_features. */
private boolean checkAllChromosomesHaveMarkers(Connection con) {
boolean result = true;
// find all the chromosomes, and for each one check that it has some
// markers
// note a "chromosome" is assumed to be a seq_region that is:
// - on the top-level co-ordinate system and
// - doesn't have and _ or . in the name and
// - has a seq_region name of less than 3 characters
// - doesn't have a name starting with "Un" or "MT"
// get top level co-ordinate system ID
String sql = "SELECT coord_system_id FROM coord_system WHERE rank=1 LIMIT 1";
String s = DBUtils.getRowColumnValue(con, sql);
if (s.length() == 0) {
System.err.println(
"Error: can't get top-level co-ordinate system for " + DBUtils.getShortDatabaseName(con));
return false;
}
int topLevelCSID = Integer.parseInt(s);
try {
// check each top-level seq_region (up to a limit) to see how many
// marker_map_locations and marker features there are
Statement stmt = con.createStatement();
ResultSet rs =
stmt.executeQuery(
"SELECT * FROM seq_region WHERE coord_system_id="
+ topLevelCSID
+ " AND name NOT LIKE '%\\_%' AND name NOT LIKE '%.%' AND name NOT LIKE 'Un%' AND name NOT LIKE 'MT%' AND LENGTH(name) < 3 ORDER BY name");
int numTopLevel = 0;
while (rs.next() && numTopLevel++ < MAX_TOP_LEVEL) {
long seqRegionID = rs.getLong("seq_region_id");
String seqRegionName = rs.getString("name");
// check marker_map_locations
logger.fine("Counting marker_map_locations on chromosome " + seqRegionName);
sql =
"SELECT COUNT(*) FROM marker_map_location WHERE chromosome_name='"
+ seqRegionName
+ "'";
int rows = DBUtils.getRowCount(con, sql);
if (rows == 0) {
ReportManager.problem(
this,
con,
"Chromosome "
+ seqRegionName
+ " (seq_region_id "
+ seqRegionID
+ ") has no entries in marker_map_location");
result = false;
} else {
ReportManager.correct(
this, con, "Chromosome " + seqRegionName + " has " + rows + " marker_map_locations");
}
// check marker_features
logger.fine("Counting marker_features on chromosome " + seqRegionName);
sql = "SELECT COUNT(*) FROM marker_feature WHERE seq_region_id=" + seqRegionID;
rows = DBUtils.getRowCount(con, sql);
if (rows == 0) {
ReportManager.problem(
this,
con,
"Chromosome "
+ seqRegionName
+ " (seq_region_id "
+ seqRegionID
+ ") has no marker_features");
result = false;
} else {
ReportManager.correct(
this, con, "Chromosome " + seqRegionName + " has " + rows + " marker_features");
}
}
rs.close();
stmt.close();
if (numTopLevel == MAX_TOP_LEVEL) {
logger.warning("Only checked first " + numTopLevel + " seq_regions");
}
} catch (SQLException se) {
se.printStackTrace();
}
return result;
}
/**
* Run the test.
*
* @param dbre The database to use.
* @return true if the test passed.
*/
public boolean run(DatabaseRegistryEntry dbre) {
boolean result = true;
Connection con = dbre.getConnection();
try {
Statement stmt = con.createStatement();
// Query returns all external_db_id-object type relations
// execute it and loop over each row checking for > 1 consecutive row with same ID
ResultSet rs =
stmt.executeQuery(
"SELECT x.external_db_id, ox.ensembl_object_type, COUNT(*), e.db_name FROM object_xref ox, external_db e, xref x LEFT JOIN transcript t ON t.display_xref_id = x.xref_id WHERE x.xref_id = ox.xref_id AND e.external_db_id = x.external_db_id AND isnull(transcript_id) GROUP BY x.external_db_id, ox.ensembl_object_type");
try {
long previousID = -1;
String previousType = "";
while (rs != null && rs.next()) {
long externalDBID = rs.getLong(1);
String objectType = rs.getString(2);
// int count = rs.getInt(3);
String externalDBName = rs.getString(4);
if (externalDBID == previousID) {
ReportManager.problem(
this,
con,
"External DB with ID "
+ externalDBID
+ " ("
+ externalDBName
+ ") is associated with "
+ objectType
+ " as well as "
+ previousType);
result = false;
}
previousType = objectType;
previousID = externalDBID;
} // while rs
} finally {
DBUtils.closeQuietly(rs);
}
stmt.close();
} catch (SQLException e) {
e.printStackTrace();
}
if (result) {
ReportManager.correct(
this, con, "All external dbs are only associated with one Ensembl object type");
}
return result;
} // run